Variant report

Variant	rs3943706
Chromosome Location	chr7:38534759-38534760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12154302	0.85[ASN][1000 genomes]
rs13239504	0.90[YRI][hapmap];0.97[AFR][1000 genomes]
rs1558617	0.87[ASN][1000 genomes]
rs17171367	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17171377	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17171384	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17171387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1861239	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2267808	0.82[JPT][hapmap]
rs2299949	0.93[JPT][hapmap]
rs2893561	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34433569	1.00[AFR][1000 genomes]
rs34523382	1.00[AFR][1000 genomes]
rs34665148	1.00[AFR][1000 genomes]
rs34789395	0.93[AFR][1000 genomes]
rs35367242	1.00[AFR][1000 genomes]
rs35375449	0.93[AFR][1000 genomes]
rs35440398	0.95[AFR][1000 genomes]
rs35978695	0.97[AFR][1000 genomes]
rs3735089	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3778876	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3778879	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3807413	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3807416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3807419	0.81[ASN][1000 genomes]
rs3807425	0.81[JPT][hapmap]
rs3807426	0.82[JPT][hapmap]
rs3823594	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41279585	0.87[ASN][1000 genomes]
rs57486020	0.82[AFR][1000 genomes]
rs66520224	0.93[AFR][1000 genomes]
rs6956760	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs71548612	0.82[AFR][1000 genomes]
rs7811601	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3943706	VPS41	cis	cerebellum	SCAN
rs3943706	AMPH	cis	Muscle Skeletal	GTEx
rs3943706	AMPH	cis	Adipose Subcutaneous	GTEx
rs3943706	AMPH	cis	Skin Sun Exposed Lower leg	GTEx
rs3943706	AMPH	cis	Nerve Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38502600-38549400	Weak transcription	Fetal Stomach	stomach
2	chr7:38524000-38543400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:38524200-38545000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:38528600-38553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:38531400-38544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:38531800-38543800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:38532000-38540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:38533200-38542800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:38534200-38542400	Weak transcription	Aorta	Aorta

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